On 08/08/2012 20:15, Rob Smith wrote:
> Is there a way (like obabel -L svg) to get the GENOPTIONS? I am
> struggling to get the -s "<substring> <color>" section to transfer
> programmatically.
The -s option is not part of SVGFormat and works on the internal OBMol
object, so you can also see the color when it is output to PNG or even
CML format. It would have an option type OBConversion::GENOPTIONS.
Obtaining its documentation is complicated by there also being a SMARTS
descriptor called s, but
obabel -L ops s
will work.
I'm not familiar with ruby syntax, but the following C++ code (without
error checking) illustrates doing a conversion with options at two
different levels.
The first is close to the command line method.
int main(int argc,char **argv)
{
std::ofstream ofs("out.svg");
std::stringstream ss("CCCO");
OBConversion conv(&ss, &ofs);
conv.SetInAndOutFormats("smi", "svg");
conv.AddOption("s", OBConversion::GENOPTIONS, "CO purple");
conv.Convert();
return 0;
}
The second is at a lower level, and it is necessary to explicitly call
DoTransformations() to apply the GENOPTIONS.
int main(int argc,char **argv)
{
OBConversion conv(&std::cin, &std::cout);
conv.SetInAndOutFormats("smi", "svg");
conv.AddOption("s", OBConversion::GENOPTIONS, "CO purple");
OBMol mol;
conv.ReadString(&mol,"CCCO");
mol.DoTransformations(conv.GetOptions(OBConversion::GENOPTIONS), &conv);
std::cout << conv.WriteString(&mol) << std::endl;
return 0;
}
I hope this helps.
Chris
>
> I've tried a lot of variants, the current one being:
> self.obconv.add_option("s #{substructure}
> red",OpenBabel::OBConversion::INOPTIONS)
>
> The goal for this option is to color the substructure red.
>
> On Tue, Aug 7, 2012 at 8:12 PM, Geoff Hutchison
> <ge...@geoffhutchison.net> wrote:
>>> characters to complete the translation of the command line argument
>>> for what I am trying to do:
>>>
>>> obabel benzodiazepine.sdf.gz -O out.svg --filter "title=3016" -s
>>> "c1ccc2c(c1)C(=NCCN2)c3ccccc3 red" -xu -d
>>
>> Keep in mind that if you're doing it programmatically, you don't use the 'x'
>> part of the flag. So that '-xu' is just "u" for your OUTOPTIONS ruby script.
>>
>> Hope that helps,
>> -Geoff
>
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